Halo: Marathon
by AvidWriter117
Summary: Written only a few months before the announcement of Cole Protocol, this tells the story of what happened to the Master Chief, Grey Team, and the SPARTANS inside the Shield World Onyx after the events of Halo 3.


**Chapter 1: Chapter 1: A New Beginning**

* * *

"_Wake me...when you need me."_

Cortana looked upon the impassive face of John, Spartan-117. He lay in a Cryo Tube, still in his Mjolnir Mark VI armor. His faceplate had been depolarized, so the soldier's face was just visible under the ice and shadow that lay between it and the outside world.

Cortana sat cross-legged upon a cylindrical pedestal, continuously watching the man's handsome, if somewhat pale, features. It had been six years since the events on the Ark and the destruction of both the Covenant and the Flood. A distress signal had been sent not long after their ship became dead in space, but no one had come. Now Cortana had no choice but to ponder the existential and sort through her overflowing memory banks.

The events upon the now destroyed Alpha Halo still ran through her circuits.

The bastard 343 Guilty Spark... How Master Chief could ever have trusted him, she would never know.

Cortana opened her eyes as she came out of her mechanically vivid memory. She stood and 'walked' off her pedestal for her usual tour of the section of the ship. As she neared the foremost part of the vessel, she slowed her pace. Coming to a stop, she looked out at the line of stars. Here, the ship had been torn in half by the firing of Alpha Halo, separating the Chief and the Arbiter. The latter was able to get through the portal before it closed forever, but the Chief and Cortana weren't so lucky.

_Had _they made it through the portal in time? If so, they would have been on Earth already. But had they not made it through the portal, the whole Milky Way Galaxy should be visible through one of the craft's view ports.

So where were they? The answer wasn't coming any time soon, Cortana knew that much.

She sat upon the ragged edge of the ship and gazed upon the stars thoughtfully. Somewhere out there, her Mother, her creator, could be waiting for her return with the greatest, if not the last, of the Spartans.

The AI reflected on all those who had died in the Human-Covenant War. The list seemed endless, but many names and faces popped to the forefront of her memories. The dozens of Spartans who had died at the hands of the Covenant; Major Silva; Captain Jacob Keyes; Miranda Keyes; Sergeant Johnson. The millions of those who had died upon the glassed planets. The thousands, if not millions, who had died upon Africa from the outbreak of Flood and its subsequent glassing by the Covenant Separatists.

There were hundreds more that flashed before Cortana's eyes, and she was forced to push the memories away or risk becoming lost in them. She stood, and continued her tour of the ship. When she was once again upon her pedestal, she began to sort through all her memory processes and stored information, tossing away all that was unnecessary, so as to leave room in case she ever discovered any new information.

"_One single flood spore can destroy a species..."_

"_...The only way to kill the Flood is to starve them to death, and that's exactly what Halo is meant to do: Wipe the Galaxy clean of all sentient life..."_

The Forerunners had built 7 Halos at strategic points across the galaxy to eliminate potential Flood hosts. The Ark had then been built far from the galaxy, and far from the reach of the Flood, with a portal leading to it upon Earth.

That was the only way to destroy the Flood, for while life is present, the Flood will seek it out.

When Alpha Halo had been destroyed, a signal reached the Ark within seconds. The Sentinels there had immediately begun reconstructing it from scratch, and was scheduled to finish within months.

But the humans interfered. The Master Chief went to the Ark, and when the Covenant mobile planet High Charity had crashed upon it, filled with Flood, he had decided to activate the Halo which had yet to be finished, thereby destroying both the Ark and the Flood.

But not all had gone according to plan.

And one example of this sat in front of the Master Chief's Cryo Tube as Cortana looked upon the stars only a few corridors away. The Flood infection form whipped its short tentacles through the air at the site of food. It moved faster than seemed possible, and was now sitting atop the Cryo Tube, attempting to crack its glass with its tiny needle-tipped limbs.

But it was unsuccessful, and was only able to leave a small scratch before it was forced to leave lest it reveal itself to unwanted eyes...

"_Assembled here tonight are all surviving Spartans, save three, who are otherwise engaged in fields of combat too distant to be easily recalled."_

**November 31, 2536; Military Calendar. Unknown Planet, Galaxy Section CVI.**

Julian, Rick, and Elise knelt upon a limestone cliff, overlooking a large Covenant encampment. Rick carried a SRS99C-S2 AM Sniper Rifle, and looked through its sleek Oracle scope.

"Why are they pulling out?" Elise said, as the Covenant soldiers were only specks in the distance.

"I'm not quite sure, but they don't seem too thrilled," Rick said, "The Brute Captain is practically screaming, from what I can tell. Woah! He just kicked off a grunts methane pack, and the sucker's flopping like a fish outta water!"

"Concentrate. I know the bastards are ugly, but try to read the Brute's lips or something," said Julian.

"I'm working on it, chill out."

Rick pressed his eye so hard into the scope of his rifle that when he pulled back again, there was a red circle around it. "I can't deduce too much, but it seems like something bad has happened... real bad. They've all been ordered to get to their Phantoms and get back to their ships." He slipped his rifle over his shoulder, and put his Mjolnir helmet back upon his head.

"Crap, then we'd better get their first, or we're gonna be in for a butt-load of trouble," Julian said.

"Aye, Aye. Hailing the dropship," Elise said, then keyed the Mic in her Helmet, "Hosky, fire up the drop ship, we're on our way."

"Aye, ma'am."

They stood as one and turned to walk back to the Pelican. It lay in a small outcrop of bushes, to hide its Olive tint. As the Spartans neared it, the Pilot inside gave them a big wave. They shook their heads at his lack of formality, but waved back nonetheless. The back hatch opened soundlessly, and the 3 noncoms stepped inside.

"So what's happening out there?" Hosky said.

"We're not quite sure, but they're pulling out," Julian said, "So we've gotta beat them to their ships."

"We're going _in_ their ships?"

"Yes, Marine. Well, actually _we're_ going in their ships," Julian waved to his Spartans, "You're just going to drop us off."

The pilot gave an audible sigh of relief, and started up the Pelican's engines. "So what do I do after that? And what are you guys gonna do when I leave?"

"_You _are going back to the _Omniscient_ while _we _destroy the Covenant Fleet and steal one of their ships."

"And...you three can do all that? Even if you're Spartans, that's one hellova mission."

"I guess we'll see," Julian said, "But I'm quite confident."

"Yah, I guess you are," Hosky replied, and with that the 'bird' lifted off and flew out into the infinite space.

Not far out of atmosphere, a Large Covenant Carrier fought the pull of gravity. It was so massive in size, that the Spartan's Pelican was only an ant in its shadow. It approached the Carrier's bay unnoticed, except by a single Grunt; who, noticing that all the soldiers that occupied the ship happened to be gone at the moment, jumped into the nearest escape pod and left the ship forever.

Inside the Pelican, Julian briefed his Spartans on the mission ahead. "Okay, the Command Center is a necessity of course, but so are the engine rooms," he said, "Since the Command Crew will most likely have body guards, two of us will be going there, while the third heads towards the Engine room."

"And do we know the schematics of this ship?" Elise said.

"No, that's the problem," Julian replied, "We will be estimating, from past experience. I have Intel that the Covenant places their Bridge at the very center of the ships, for the most possible protection. I would also assume that they would put their engines at the back, for obvious reasons."

"Agreed, that doesn't seem to hard to put together," Rick said, "This'll be a piece of cake."

"Of all the things this mission is going to be, a Piece of cake is not one of them."

* * *

"_Didn't you know? Spartans never die."_

Fred, Spartan 104; Kelly, Spartan 078; and Linda, Spartan 058, stood upon the bridge of the Marathon-Class Cruiser _Olympus._ They wore brand new Mjolnir Mk VII Armor, and each carried a different new Mjolnir Helmet, which suited their skills. Fred carried a personalized 'Hayabusa' helmet, to instill fear into the enemy. Kelly carried a 'Recon' Helmet, which was light and would help her vision while running. Linda carried a 'Scout' Helmet, to facilitate her sniping abilities by filtering out external distractions.

The new armor had been given to them two days prior, and had yet to be used in battle, or even worn at all. The Spartans had thought they were so cool when they first got them, but now they seemed so... alien.

But they were satisfied, in most aspects. The rest of the armour performed superbly in all tests. The shields were twice as strong as the old ones, the distance of the motion and heat detectors were raised from fifteen feet to thirty. The gel layer could taper to a hair thin, or up to 3 inches thick. Communications devices were much stronger, though that was immeasurable. There were also specializations of each Armor Permutation to suite each individual Spartan's needs. The most important change, however, was AI integration.

Due to all soldiers, technicians, and scientists that were mortally wounded in the Human-Covenant wars, organ donations numbers increased dramatically. Some brains were used to create Smart AI's, which were distributed to almost all of the UNSC populace. The Spartans got first pick. Each received the best AI's the UNSC had to offer, which could be slipped in and out of the Spartan's helmets at their discretion. Fred carried AI _Durandal_, who had a knack for putting clues together and deciding what to do. Kelly chose the AI _Leela, _who had the ability to boost the Armor's strength capabilities for faster running. Linda held the AI _Tycho_, who could magnify the Mjolnir Faceplate 6 times the normal, and had very skilled translation software.

The three Spartan IIs ordered a Slipspace jump as soon as the generators were charged, then retreated to their cabin. Inside the large room, boxes upon boxes of weapons, supplies, and armour were stacked against all the walls. Each had been sorted, resorted, and sorted again, to ensure that nothing in this mission would go wrong.

Too much had gone wrong on previous missions.

* * *

"The LZ is hot," Hosky said, "My radar catches a shade emplacement on the far corner of the bay, manned by an Elite. This bird won't hold on too much against that firepower, make sure to cut out quick."

"Can do, Hosky," Rick said, "Thanks for everything."

"So long, boys."

The pilot backed quickly into the Covenant Carrier's launch bay, and lowered the hatch. It took a few seconds, but before the Spartan's feet touched the ground, the Shade Emplacement was firing upon their position. The pilot closed the Pelican's hatch and pulled out of the ship's bay.

Julian, being the quickest of the group, ran around a pillar on the far side of the shallow bay and pulled his M6D pistol from his hip. It took almost a whole clip at the alien's head to bring him down, spraying purple blood over the deck. The Spartan slipped his pistol back onto his hip, and pulled his MA5B from his back.

By the time the soldiers had crossed the bay, more Covenant had poured from the doors at all sides, attracted by the sound of battle. Green can not hide well among walls of deep purple, but the Spartans made use of all the cover they could find. Rick focused his M6D upon the Elites, who stood tall above the rest. Grunts fell to the ground writhing as their Methane breathing tubes were cut by the invisible hand of Elise. Julian, who felt that stealth had already been abandoned, yanked the dead Elite out of the Shade and climbed inside the blood soaked seat. Making sure that neither Elise nor Rick were in his line of fire, Julian pushed the firing studs.

Purple fire rained down upon the Covenant's sloppy formation. It tore through the grunts and Jackals like a knife through tissue paper, igniting the methane-breather's packs and sending them skidding across the floor. Elites shot their Plasma Rifles at the intruder, but the weapons splashed uselessly over the Shade's base, and they, too, were cut down.

Soon the bay was littered with Alien bodies, and the Spartan's advance was uncontested. A half minute was spent salvaging the weapons off the dead, and they soon moved forward. They passed through a wide door, which opened at their approach, and entered the useless honeycomb of hallways that was always associated with the large Covenant craft. Their metal boots rang out on the colorful metal, and passed through bizarrely empty corridors.

"Where've they all gone?" Rick asked.

"They all left the ship, remember?" Elise said, "They're probably on their way here right now. Let's hope the alarms haven't been raised."

The other two silently concurred, and the group entered a circular room with a pillar down the middle, took a right, and walked up a long ramp. Here, their path split three ways, straight forward or to either side. Without saying anything, the group split up, each going a different way. Julian, going left, paused at a doorway, his rifle at the ready, and waved his hand in front of its motion sensor to activate it.

His caution was rewarded as an Elite in red armour primed a plasma grenade and hurled it down the corridor toward the Spartan. Julian ducked under the glowing sphere and charged at the Elite. Its plasma rifle hung uselessly at its side, for it had not expected the grenade to miss, and Julian rammed his shoulder into the alien's stomach. It grunted and fell to the ground, where Julian lifted his half-ton boot and brought it down heavily on the Elites face, breaking two of its mandibles.

The alien howled in pain, giving the Spartan the opportunity to shove the barrel of his rifle into the Elite's gaping mouth and fire half a clip into its gullet. The beast died instantly, and purple blood seeped from the wound to coat the already purple floor.

Julian pushed forward, stopping only to pilfer the Elite's plasma rifle and a plasma grenade. When he passed the next door, however, he was confronted by a _new_ type of Covenant. It was roughly a meter in diameter, with six long tentacles and eyes, and it floated about two feet above the ground. Knowing the simple engineers were harmless, Julian stepped around it and walked along a long corridor.

As he turned around a corner, yet another plasma grenade came whizzing over his head. It bounced off the wall behind him, and glued itself to the shining floor. The Spartan jumped away from the explosion, rushed down the hall, with plasma rifle and pistol fire pouring down toward him.

Four Grunts and two Elites waited for him at the end. Three small globules of green plasma splashed over his chest plate, boiling away one of the many layers of titanium alloy. Julian lobbed his plasma grenade into the midst of the group. It latched onto of the Elite's shins, who roared and shook its fists at the soldier.

Two of the grunts were taken out with the Elite, but the other two and the last Elite were able to get away before the explosion, and continued to rain fire down upon Julian's position.

The noncom rolled to his right, and came up spraying his Assault Rifle blindly. 'Spray and Pray', it was called, and it normally worked quite well. This was no exception, as the two grunts were taken down almost instantly, and the Elite's shields flickered and failed. The alien roared in defiance, and fired his blue plasma rifle until it overcharged.

But the Spartan was still standing, and had already slammed a fresh clip into his Rifle. The Elite had time for a slight look of puzzlement before it fell to the ground dead.

"Alpha 2 to Alpha 1," Elise's voice called out over Julian's comm. system, "I am nearing the Command Center. Be advised, hostiles are on the move. I have intercepted communications; they are heading your way. Over."

"Acknowledged, Alpha 2," Julian replied, "I'll keep an eye out for them. Over." Switching comm. channels, he said, "Alpha 3, what is your status? Over."

"I'm pretty good," Rick's voice called out, louder then necessary, "These Coveys and I are having a little tea party! Oddly enough, they serve it out of their chests, and its bright purple!"

"Where are you?"

"...I have no idea, sir. I think I'm not too far from the command center, but I can't be sure in this god forsaken ship."

"Good. Try to make your way towards the Command Center. You should be able to deduce its location by the Covenant soldiers that are running _away_ from it."

"Yes, sir. I'm on my way."

"Alpha 1 out."

Julian ran into no opposition on his way toward the engine room.

And no wonder. As he walked through the large set of double doors that signified the room's entrance, he came face to face with what seemed like a whole battalion of Covenant Forces.

"Oh...hello," Julian said, to the nearest Brute, before its massive fist slammed into his visor.

"Julian, come in!" Elise yelled into her comm. No one replied. "Rick, get the hell down there and see what happened."

"On it," Rick said. He sprinted out of the room. It took only 20 minutes to reach the engine room, despite the ship's size and twisting corridors. As he rounded a corner that lead to its main room, he noticed that the door at the far end was melted off. A dead grunt lay beside it, for reasons unknown.

The butt of his rifle clicked as it hit his shoulder armour. His finger eased gently onto the trigger, and he clicked off the safety.

Elites never killed grunts, unless there was a mutiny. There must be Brutes.

His assumption was proved correct. As he walked through the door, two massive hands closed around his neck and attempted to throttle him. An elbow to the beast's torso loosened the grip, but only slightly. It took a metal boot to groin for the grip to ease enough to make a difference, which Rick too advantage of. He pried the fingers off his neck with his loose hand, twisted away, and fired point blank with his Assault Rifle into the Brute's chest. It howled and fell backward, spraying dark red blood across Rick's armour.

As he turned, he was met by another Brute.

Then yet another.

And another.

"Elise."

"Yes, Rick?"

"We're all clear. There are no Brutes in sight. We have free reign of the ship, from my viewpoint."

"Is Julian OK?" Elise said.

"I'm here. A bit bruised up, but ready for a fight," Julian's voice rang over the comm.

"Good. OK, Grey Team; Lets see what this baby can do."

* * *

And there it was: a way to survive.

A planet, roughly the size of earth, could be seen in the distance. A lot of its surface was covered in forests, but great cities were also visible. A great civilization outside the galaxy's rim? It was definitely possible, but unlikely.

'_Wake me...when you need me.'_

Well, the Master Chief was needed.


End file.
